[AMBER] When and how is leap re-numbering residues?

From: Jan-Philip Gehrcke <jgehrcke.googlemail.com>
Date: Tue, 12 Jul 2011 15:27:19 +0200


I don't have a feature request like "keep the residue numbers from the
original PDB file!", but I'd rather understood how the leap residue
numbering scheme actually works, because I don't quite get it and I have
the feeling that there is a lack of documentation and other references
on the web.

What irritates me that in a work flow there may be at least three
different numbering schemes:
1) the residue numbering from the original PDB file
2) the leap-internal residue numbering _directly after_ invoking `loadpdb`
3) the numbering of PDB files written by leap after invoking `savepdb`

I assume this is correct so far.

Just an example how that could look like:
regarding 1) conside two chains (A and B) being in the original PDB
file. Let r be the lowest residue number within both chains. There may
be gaps in the numbering sequence.
regarding 2) after `loadpdb`, the lowest residue number will still be r,
right? But the residues of one of the chains (or both?) get re-numbered
to some higher values, because leap does not support chains. Are gaps
regarding 3) the lowest residue number will always be 1. What I've seen
so far, there never are any gaps in the resulting numbering.

Now, what do the docs say? (AmberTools docs from April 7th, 2011)

Regarding `loadpdb`: "The sequence numbers of the RESIDUEs will be
determined from the order of residues within
the PDB file ATOM records"

This is a quite general statement. From this sentence I would expect
that the numbering starts at 1 and gaps are closed. The real behavior
seems to be different.

Regarding `savepdb`: Nothing is noted with respect to a re-numbering.
But leap actually seems to re-number during `savepdb`.

This is just what I observed after playing around a bit. For sure, I was
not able to discover leap's entire numbering behavior correctly.
Unfortunately, the docs don't seem to tell everything. So, in order to
predict leap's behavior I would like to ask you:

When exactly does leap perform re-numbering? Which rules are applied
during this re-numbering? Why does this make sense?

Thanks a lot :-)


Jan-Philip Gehrcke
PhD student
Structural Bioinformatics Group
Technische Universitšt Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
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Received on Tue Jul 12 2011 - 06:30:02 PDT
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